Cystic fibrosis transmembrane conductance regulator gene mutations

ABSTRACT

The present invention provides novel mutations of the CFTR gene related to cystic fibrosis or to conditions associated with cystic fibrosis. The mutations include duplication of exons including duplication of exons 6b through 10. Methods of identifying if an individual contains the exons 6b through 10 duplication are provided as well as nucleic acid fragments that contain the junction site of the duplicated segment. The detection of additional mutations in the CFTR gene are also provided.

This application claims priority under 35 USC § 119(e) to provisionalapplication Ser. No. 60/709,329 filed Aug. 18, 2005, the entire contentsof which are incorporated by reference herein.

BACKGROUND OF THE INVENTION

The following description of the background of the invention is providedsimply as an aid in understanding the invention and is not admitted todescribe or constitute prior art to the invention.

The present invention relates to a novel cystic fibrosis transmembraneregulator (CFTR) gene mutation and its use in the diagnosis of cysticfibrosis. Cystic fibrosis (CF) is the most common severe autosomalrecessive genetic disorder in the Caucasian population. It affectsapproximately 1 in 2,500 live births in North America (Boat et al, TheMetabolic Basis of Inherited Disease, 6th ed, pp 2649-2680, McGraw Hill,NY (1989)). Approximately 1 in 25 persons are carriers of the disease.The responsible gene has been localized to a 250,000 base pair genomicsequence present on the long arm of chromosome 7. This sequence encodesa membrane-associated protein called the “cystic fibrosis transmembraneregulator” (or “CFTR”). There are greater than 1,000 different mutationsin the CFTR gene, having varying frequencies of occurrence in thepopulation, presently reported to the Cystic Fibrosis Genetic AnalysisConsortium. These mutations exist in both the coding regions (e.g.,ΔF508, a mutation found on about 70% of CF alleles, represents adeletion of a phenylalanine at residue 508) and the non-coding regions(e.g., the 5T, 7T, and 9T mutations correspond to a sequence of 5, 7, or9 thymidine bases located at the splice branch/acceptor site of intron8) of the CFTR gene. Comparison of the CFTR genomic and cDNA sequencesconfirms the presence of 27 exons. The exons are numbered 1, 2, 3, 4, 5,6a, 6b, 7, 8, 9, 10, 11, 12, 13, 14a, 14b, 15, 16, 17a, 17b, 18, 19, 20,21, 22, 23, and 24. Each intron is flanked by the consensus GT-AGsplice-site sequence as previously reported (Zielenski, et al., (1991)Genomics 10, 214-228).

The major symptoms of cystic fibrosis include chronic pulmonary disease,pancreatic exocrine insufficiency, and elevated sweat electrolytelevels. The symptoms are consistent with cystic fibrosis being anexocrine disorder. Although recent advances have been made in theanalysis of ion transport across the apical membrane of the epitheliumof CF patient cells, it is not clear that the abnormal regulation ofchloride channels represents the primary defect in the disease.

Methods for detecting CFTR gene mutations have been described. See e.g.,Audrezet et al., “Genomic rearrangements in the CFTR gene: extensiveallelic heterogeneity and diverse mutational mechanisms” Hum Mutat. 2004April; 23(4):343-57; PCT WO 1004/040013 A1 and corresponding USapplication #20040110138; titled “Method for the detection of multiplegenetic targets” by Spiegelman and Lem; US patent application No.20030235834; titled “Approaches to identify cystic fibrosis” by Dunlopet al.; and US patent application No. 20040126760 titled “Novelcompositions and methods for carrying out multiple PCR reactions on asingle sample” by N. Broude.

A variety of CFTR gene mutations are known, and the identification ofadditional mutations will further assist in the diagnosis of cysticfibrosis.

SUMMARY OF THE INVENTION

The inventors have discovered a new mutation in the CFTR gene thatresults in a duplication of exons 6b through 10 and leads to cysticfibrosis or is associated with conditions associated with cysticfibrosis. By “conditions associated with cystic fibrosis” is meant anyclinical symptoms that may be found in a cystic fibrosis patient and aredue to one or more CF mutations.

In a one embodiment, the duplicated segment containing exons 6b-10represents about 26,817 base pairs (bp). In another embodiment, theduplicated segment is 26,817 base pairs, defined asgIVS6a+415_IVS10+2987Dup26817 bp in accordance with guidelines from theHuman Genome Variation Society. The duplicated 26,817 bp segment beginsat position 415 of the CFTR intron 6a and ends at position 2987 of theCFTR intron 10. The duplicated region is inserted between IVS10+2,987and IVS10+2,988 and which results in a unique junctionIVS10+2,987/IVS6a+415. The term “IVS6a+415” is a shorthand identifierfor position 415 measured from the start of intron 6a, while the term“IVS10+2,987” is a shorthand identifier for position nucleotide position2,987 measured from the start of intron 10. The term “Dup ex 6b-10” isused herein as a shorthand for gIVS6a+415_IVS10+2987Dup26817 bp. Thenucleotide positions of the exons and introns for the human CFTR gene isshown in FIG. 1.

The unique junctions generated by duplications of exon 6b-10 generatesnew amino new sequence. For example, Dup ex 6b-10 of the CFTR generesults in an out-of-frame addition of 8 amino acids after codon E528 ofexon 10, encoding a new C-terminal sequence between 529 and 536(Arg-Ser-Glu-Ser-Trp-Glu-Asp-Glu; SEQ ID NO:1), followed by a TGA Stopcodon. The result is a truncated CFTR protein lacking the terminal NBD1domain and beyond and having an 8 mer non-CFTR gene C-terminal far endsequence (SEQ ID NO:1). Dup ex 6b-10 of the CFTR gene causes earlytruncation of the protein product, resulting in a nonfunctional CFTRprotein.

The present invention provides a method of detecting if a CFTR gene innucleic acid from an individual has a duplication of exons 6b through 10by detecting the duplication of at least one portion of exons 6b through10.

The present invention also provides a method of screening a subject todetermine if the subject is a CF carrier or a CF patient, the methodcomprising determining if a CFTR gene in nucleic acid from theindividual has a duplication of exons 6b through 10 by detecting theduplication of at least one portion of exons 6b through 10.

The present invention further provides a method of determining if anindividual is predisposed to cystic fibrosis or a condition associatedwith cystic fibrosis, the method comprising determining if a CFTR genein nucleic acid from the individual has a duplication of exons 6bthrough 10 by detecting the duplication of at least one portion of exons6b through 10.

The present invention still further provides a method of counseling anindividual on the likelihood of having an offspring afflicted withcystic fibrosis or a condition associated with cystic fibrosis, themethod comprising determining if a CFTR gene in nucleic acid from theindividual has a duplication of exons 6b through 10 by detecting theduplication of at least one portion of exons 6b through 10.

In any of above methods, a sequence from the CFTR gene may be amplifiedand the amplified sequence tested for the presence of the duplication.In a preferred approach, amplification is by the polymerase chainreaction.

In another embodiment, the exon 6b-10 duplication of the CFTR gene isdetected by (a) amplifying sequence from one or more of exon 6b, 7, 8,9, and 10 from nucleic acid from the individual; (b) identifying theamplified exon sequence; and (c) comparing the amount of each amplifiedexon sequence versus that similarly amplified for a normal CFTR gene,wherein a substantial increase in the amount of amplified exon sequenceobserved versus that for a normal CFTR gene indicates a duplication ofexon 6b-10. The exon sequence is preferably amplified usingoligonucleotide primer pairs that hybridize upstream and downstream ofthe exon sequence to be amplified. Preferably, sequence from most or allof exons 6b, 7, 8, 9, and 10 are amplified and evaluated. The exonsequence may be amplified using primers specific to intron or exonsequence. Sequence may be amplified from introns instead of or inaddition to sequence from the corresponding exon and then used forcomparison with that of a similarly amplified sequence from wildtypenucleic acid. If multiplex amplification is desired, one primer of eachprimer pair may be detectably labeled to allow discrimination of thedifferent amplified products. In this method, amplification ispreferably conducted in the linear phase (e.g. SQF PCR).

Sequence representing exons may be amplified using primers for one ormore introns within the duplicated 6b-10 segment and compared to thatsimilarly amplified from a normal gene. Sequence also may be amplifiedfrom introns instead of or in addition to sequence being amplified fromexons.

In yet another embodiment, the exon 6b-10 duplication of the CFTR geneis detected by amplifying with primers that flank the unique junctionformed between introns 10 and 6a created by the duplication. The forwardprimer is complementary to sequence upstream (3′) of the junction whilethe reverse primer is complementary to sequence downstream of thejunction. The distance between the forward and reverse primers arechosen to optimize the size of the product amplified or to achievedetection by a Real Time PCR method such as the TaqMan system. Inanother embodiment, the junction fragment is detected by agarose gelelectrophoresis. In this embodiment, the size of the junction fragmentcan vary depending on where the forward and reverse primers that flankthe duplication are placed. In mutations where the junction isIVS10+2,987:IVS6a+415, the forward primer is complementary to sequenceupstream of IVS10+2987 and the reverse primer is complementary tosequence downstream of IVA6a+415. In a further embodiment, amplifiedproduct may be sequenced to verify the 6b-10 junction.

In a further embodiment, the exon 6b-10 duplication of the CFTR gene isdetected using MLPA (i.e., multiplex ligation-dependent probeamplification) or MAPH (i.e., multiplex amplifiable probehybridization).

In another embodiment, the exon 6b-10 duplication of the CFTR gene isdetected by amplifying with primers that flank the 6b-10 segment. In oneapproach, a forward primer is used hybridizing to a segment precedingIVS6a+415 and a reverse primer is used hybridizing to a segmentfollowing IVS10+2987. Such analysis of a wild-type CFTR gene willamplify a product that includes 26,817 bp while a duplication of exons6a through 10 in one allele will result in two fragments, one of whichincludes the 26,817 representing the single 6b-10 segment and a fragmentwhich includes 53,634 bp containing the duplication (i.e.6b-10-6b′-10′). By locating the primers close to IVS6a+415 andIVS10+2987, the resulting amplified products will approach the size ofthe target 6b-10 segment (26,817 bp) and the size of the 6b-10-6b′-10′segment (54,634 bp). For example, primers located very close to thespecified sites will amplify from the normal CFTR gene a product ofabout 26,817 bp and from the CFTR gene with a Dup ex 6b-10 mutation, aproduct of about 53,634 bp.

The term “about” is used herein to refer to +/−5% of a given measurementunless otherwise indicated.

In any of the above embodiments where amplification is employed,RealTime PCR can be used to detect amplification of any exons, intronsor segments thereof or the duplication junction created by the 6b-10duplication of the CFTR gene. The positioning of the primers and the useof TaqMan system probes can be detected using an automated fluorescencedetection device (e.g. Applied Biosystems 7900). In a differentembodiment the duplication of exons 6b-10 can be detected using increasein signal and cycle threshold on the TaqMan system (or equivalent) afteramplification of any one or more of exons 6b-10 or intron fragments andcomparing to normal sample. In this embodiment the use of an internalcontrol for signal normalization may or may not be utilized.

In a further embodiment, the exon 6b-10 duplication of the CFTR gene isdetected by Southern Blot analysis.

In another embodiment, the exon 6b-10 duplication of the CFTR gene canbe detected by detecting a unique protein C-terminal sequence thatresults from the duplication. For example, the Dup ex 6b-10 mutation isidentified by detecting the C-terminal sequenceArg-Ser-Glu-Ser-Trp-Glu-Asp-Glu (SEQ ID NO:1) between 529 and 536 of theCFTR protein encoded by the CFTR gene with the Dup ex 6b-10 mutation. Inone embodiment, an antibody specific for the CFTR product containing theunique C-terminal amino acid sequence (e.g. SEQ ID NO: 1) is used todetect the truncated CFTR protein in a sample from an individual.Specific binding of the antibody to the truncated CFTR gene productresulting from the exon 6b-10 duplication may be detected by ELISA,radioimmunoassay, and the like.

In any of the above methods, amplified product may be separated by size.In a further embodiment, size separation may be performed by gelelectrophoresis. In yet a further embodiment, size separation may beperformed by capillary electrophoresis.

In any of the above methods, at least one primer of each primer pair foramplification is detectably labeled with a detectable moiety.

Also provided herein are nucleic acid fragments containing the uniquejunction between exons 10 and 6b′ that occur as a result of the exon6b-10 duplication. The fragments are about 26 kb or less and include theintron 10 to intron 6a junction formed as a result of the exon 6b to 10duplication of the CFTR gene. The junction includes a sequence with atleast nine nucleotides directly adjoining each side of the junction. Inone embodiment, the sequence with at least nine nucleotides directlyadjoining each side of the junction is CATGGTGGG:CCCGGCCTA (SEQ ID NO:2) (the junction between the intron 10 and intron 6a is depicted by thesymbol “:”). In another embodiment, the sequence with at least ninenucleotides directly adjoining each side of the junction isGAGCATGGTGGG:CCCGGCCTAAAA (SEQ ID NO: 3). In yet another embodiment, thesequence with at least nine nucleotides directly adjoining each side ofthe junction is GTGTAGTGAGCATGGTGGG:CCCGGCCTAAAAAATACTT (SEQ ID NO: 4).

In an embodiment, the detection can be accomplished by amplifying thejunction fragment and performing restriction enzyme digestion thatrecognizes the junction sequence, e.g. ApaI which recognizes thesequence GGG:CCC. In a further embodiment, the detection of theduplication can be accomplished by analyzing using Arrays (exon arrays,SNP arrays, and the like) or by linkage analysis of variable polymorphicmarkers.

Other known CFTR mutations may be evaluated in nucleic acid samplesalong with that of the 6b-10 duplication are described in U.S. patentapplication Ser. No. 11/074,903 titled “Cystic Fibrosis Gene Mutations”and filed Mar. 7, 2005 and in U.S. Publication no. 20050059035 (Mar. 17,2005) by Huang et al. These and other known mutations in the CFTR genemay be determined by any of a variety of well known methods used todetect single base changes (transitions and/or smalldeletions/insertions) or by any of a variety of well known methods usedto detect exon duplication or deletion. Thus, genomic DNA may beisolated from the individual and tested for the CF mutations. In anotherapproach, mRNA can be isolated and tested for the CF mutations. Testingmay be performed on mRNA or on a cDNA copy.

Methods for amplifying multiple target segments of the CFTR gene in asingle vessel using oligonucleotide primer pairs specific to each of thetarget segments in a multiplex polymerase chain reaction (PCR) can beused as described in U.S. patent Ser. No. 10/942,257 titled “Method ofdetecting cystic fibrosis” filed Sep. 16, 2004. This multiplexamplification, which can detect one or more or all of the 27 exons ofthe CFTR gene, may also include a primer pair for at least one internalcontrol target segment of nucleic acid that does not correspond to theCFTR gene. In a preferred embodiment, the internal controls can besegments of various genes. Such segments can include an exon from theTay Sachs HEXA gene, an exon from coagulation factor II gene and/or anexon from the coagulation factor V gene. Other internal controls can beused. Preferably, the internal controls reside on different chromosomesfrom the CFTR gene, or on the short arm of chromosome 7.

Following amplification, the various target segments are separatelyidentified and evaluated for the relative amount of the segment presentversus that for a control (i.e., wildtype) CFTR gene. In a preferredembodiment, the amplified segments are separated by size such as by gelelectrophoresis and or by color.

A substantial increase in the amount of a CFTR target segment identifiedmeans that the segment has been duplicated while a substantial decreasein the amount of a CFTR target segment identified means that the targetsegment has been deleted. The term “substantial decrease” or“substantial increase” means a decrease or increase of at least about30-50%. Thus, deletion of a single CFTR exon would appear in the assayas a signal representing for example of about 50% of the same exonsignal from an identically processed sample from an individual with awildtype CFTR gene. Conversely, amplification of a single exon wouldappear in the assay as a signal representing for example about 150% ofthe same exon signal from an identically processed sample from anindividual with a wildtype CFTR gene.

In a preferred embodiment, at least one primer of each primer pair inthe PCR is labeled with a detectable moiety. Thus, followingamplification, the various target segments can be identified by size andcolor. The detectable moiety is preferably a fluorescent dye. In someembodiments, different pairs of primers in a multiplex PCR may belabeled with different distinguishable detectable moieties. Thus, forexample, HEX and FAM fluorescent dyes may be present on differentprimers in the multiplex PCR and associated with the resultingamplicons. In other embodiments, the forward primer will be labeled withone detectable moiety, while the reverse primer will be labeled with adifferent detectable moiety, e.g. FAM dye for Forward primer and Hex duefor Reverse primer. Use of different detectable moieties is useful fordiscriminating between amplified products which are of the same lengthor are very similar in length. Thus, in a preferred embodiment, at leasttwo different fluorescent dyes are used to label different primers usedin a single amplification. In still another embodiment, the normal (wt)control primers can be labeled with one moiety, while the patient (ortest sample) primers can be labeled with a different moiety, to allowfor mixing of both samples (post PCR) and the simultaneous detection andcomparison of signals of normal and test sample. In a modification ofthis embodiment, the primers used for wt samples and patient samples canbe switched to allow for further confirmation of results.

Analysis of amplified products from multiplex PCR reactions can beperformed using an automated DNA analyzer such as an automated DNAsequencer (e.g., ABI PRISM 3100 Genetic Analyzer) which can evaluate theamplified products based on size (determined by electrophoreticmobility) and/or respective fluorescent label.

In another aspect, the present invention provides kits for one of themethods described herein. In various embodiments, the kits contain oneor more of the following components in an amount sufficient to perform amethod on at least one sample: one or more primers of the presentinvention, one or more devices for performing the assay, which mayinclude one or more probes that hybridize to a mutant CF nucleic acidsequence, and optionally contain buffers, enzymes, and reagents forperforming a method of detecting a genotype of cystic fibrosis in anucleic acid sample.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 identifies the boundaries of the various exons and introns forthe CFTR gene. This data for particular regions of the gene wereobtained from GenBank using accession #s AC000111 and AC000061 as shown.

FIG. 2 is a schematic showing the CFTR gene structure for an individualwith an exon 6b-10 duplication. The duplicated exons are identified 6b′,7′, 8′, 9′ and 10′. The arrows indicate one location of PCR primersdesigned to amplify across the unique junction.

DETAILED DESCRIPTION OF THE INVENTION

By the present invention, there are provided methods for detecting amutation of the CFTR gene which is a duplication of exons 6b-10 and forusing this information to assist in clinical diagnosis of CFTR diseaseor carrier status and for genetic consuling.

By “mutations of the CFTR gene” or “mutant CF sequence” is meant one ormore CFTR nucleic acid sequences that are associated or correlated withcystic fibrosis. The nucleic acid sequences containing CF mutations arepreferably DNA sequences, and are preferably genomic DNA sequences;however, RNA sequences such as mRNA or hnRNA may also contain nucleicacid mutant sequences that are associated with cystic fibrosis. Thepresence of CF mutations described herein can be determined in a nucleicacid by sequencing appropriate portions of the CFTR gene containing themutations sought to be detected. In another approach, CF mutations thatchange susceptibility to digestion by one or more endonucleaserestriction enzymes may be used to detect the mutations. Other mutationapproaches include allele specific amplification, sequencing by primerextension, oligonucleotide ligation and specific hybridization. Thesemethods are merely exemplary of those that can be used to detect CFmutations described herein.

By “carrier state” is meant a person who contains one CFTR allele thatis a mutant CF nucleic acid sequence, but a second allele that is not amutant CF nucleic acid sequence. CF is an “autosomal recessive” disease,meaning that a mutation produces little or no phenotypic effect whenpresent in a heterozygous condition with a non-disease related allele,but produces a “disease state” when a person is homozygous, i.e., bothCFTR alleles are mutant CF nucleic acid sequences. A carrier status iswhether or not one is a carrier.

By “primer” is meant a sequence of nucleic acid, preferably DNA, thathybridizes to a substantially complementary target sequence and isrecognized by DNA polymerase to begin DNA replication. The term primeras used herein includes all forms of primers that may be synthesizedincluding peptide nucleic acid primers, locked nucleic acid primers,phosphorothioate modified primers, labeled primers, and the like.

By “substantially complementary” is meant that two sequences hybridizeunder stringent hybridization conditions. The skilled artisan willunderstand that substantially complementary sequences need not hybridizealong their entire length. In particular, substantially complementarysequences comprise a contiguous sequence of bases that do not hybridizeto a target sequence, positioned 3′ or 5′ to a contiguous sequence ofbases that hybridize under stringent hybridization conditions to atarget sequence.

By “flanking” is meant that a primer hybridizes to a target nucleic acidadjoining a region of interest sought to be amplified on the target. Theskilled artisan will understand that preferred primers are pairs ofprimers that hybridize 3′ from a region of interest, one on each strandof a target double stranded DNA molecule, such that nucleotides may beadd to the 3′ end of the primer by a suitable DNA polymerase. Primersthat flank mutant CF sequences do not actually anneal to the mutantsequence but rather anneal to sequence that adjoins the mutant sequence.In particular, primers that flank a CF exon are generally designed notto anneal to the exon sequence but rather to anneal to sequence thatadjoins the exon (e.g. intron sequence). However, in some cases,amplification primer may be designed to anneal to the exon sequence.

By “isolated” a nucleic acid (e.g., an RNA, DNA or a mixed polymer) isone which is substantially separated from other cellular componentswhich naturally accompany such nucleic acid. The term embraces a nucleicacid sequence which has been removed from its naturally occurringenvironment, and includes recombinant or cloned DNA isolates,oligonucleotides, and chemically synthesized analogs or analogsbiologically synthesized by heterologous systems.

By “crude” a nucleic acid represents at or less than 50% of a nucleicacid in a sample. Crude nucleic also encompasses nucleic acid in celllysates. The nucleic acid sample may exist in solution or as a drypreparation.

By “substantially pure” a nucleic acid, represents more than 50% of thenucleic acid in a sample. The nucleic acid sample may exist in solutionor as a dry preparation.

By “complement” and like words, e.g., “complementary” and“complementarity”, is meant the complementary sequence to a nucleic acidaccording to standard Watson/Crick pairing rules. For example, asequence 5′-GCGGTCCCA-3′ has the complement 5′-TGGGACCGC-3′. Acomplement sequence can also be a sequence of RNA complementary to theDNA sequence or its complement sequence, and can also be a cDNA. Certainbases not commonly found in natural nucleic acids may be included in thenucleic acids described herein; these include, for example, inosine,7-deazaguanine, Locked Nucleic Acids (LNA), and Peptide Nucleic Acids(PNA). Complementary need not be perfect; stable duplexes may containmismatched base pairs, degenerative, or unmatched bases. Those skilledin the art of nucleic acid technology can determine duplex stabilityempirically considering a number of variables including, for example,the length of the oligonucleotide, base composition and sequence of theoligonucleotide, ionic strength and incidence of mismatched base pairs.A complement sequence can also be a sequence of RNA complementary to theDNA sequence or its complement sequence, and can also be a cDNA.

The term “substantially complementary” as used herein means that twosequences hybridize under stringent hybridization conditions. Theskilled artisan will understand that substantially complementarysequences need not hybridize along their entire length. In particular,substantially complementary sequences comprise a contiguous sequence ofbases that do not hybridize to a target sequence, positioned 3′ or 5′ toa contiguous sequence of bases that hybridize under stringenthybridization conditions to a target sequence.

The term “stringent hybridization conditions” as used herein refers tohybridization conditions at least as stringent as the following:hybridization in 50% formamide, 5×SSC, 50 mM NaH₂PO₄, pH 6.8, 0.5% SDS,0.1 mg/mL sonicated salmon sperm DNA, and 5×Denhart's solution at 42° C.overnight; washing with 2×SSC, 0.1% SDS at 45° C.; and washing with0.2×SSC, 0.1% SDS at 45° C. In another example, stringent hybridizationconditions should not allow for hybridization of two nucleic acids whichdiffer over a stretch of 20 contiguous nucleotides by more than twobases.

By “coding sequence” is meant a sequence of a nucleic acid or itscomplement, or a part thereof, that can be transcribed and/or translatedto produce the mRNA for and/or the polypeptide or a fragment thereof.Coding sequences include exons in a genomic DNA or immature primary RNAtranscripts, which are joined together by the cell's biochemicalmachinery to provide a mature mRNA. The anti-sense strand is thecomplement of such a nucleic acid, and the encoding sequence can bededuced therefrom.

By “non-coding sequence” is meant a sequence of a nucleic acid or itscomplement, or a part thereof, that is not transcribed into amino acidin vivo, or where tRNA does not interact to place or attempt to place anamino acid. Non-coding sequences include both intron sequences ingenomic DNA or immature primary RNA transcripts, and gene-associatedsequences such as promoters, enhancers, silencers, etc.

Nucleic acid suspected of containing mutant CF sequences are amplifiedusing one or more primers that flank the mutations under conditions suchthat the primers will amplify CFTR fragments containing the mutations,if present. The oligonucleotide sequences in Table 2 are useful foramplifying segments of the CFTR gene which contain the mutations inTable 1. Nucleic acid from an individual also could be tested for CFTRmutations other than those in Table 1.

The method of identifying the presence or absence of mutant CF sequenceby amplification can be used to determine whether a subject has agenotype containing one or more nucleotide sequences correlated withcystic fibrosis. The presence of a wildtype or mutant sequence at eachpredetermined location can be ascertained by the invention methods.

By “amplification” is meant one or more methods known in the art forcopying a target nucleic acid, thereby increasing the number of copiesof a selected nucleic acid sequence. Amplification may be exponential orlinear. A target nucleic acid may be either DNA or RNA. The sequencesamplified in this manner form an “amplicon.” While the exemplary methodsdescribed hereinafter relate to amplification using the polymerase chainreaction (“PCR”), numerous other methods are known in the art foramplification of nucleic acids (e.g., isothermal methods, rolling circlemethods, etc.). The skilled artisan will understand that these othermethods may be used either in place of, or together with, PCR methods.

Nucleic acid suspected of containing mutant CF sequence may be obtainedfrom a biological sample. By “biological sample” is meant a sampleobtained from a biological source. A biological sample can, by way ofnon-limiting example, consist of or comprise blood, sera, urine, feces,epidermal sample, skin sample, cheek swab, sperm, amniotic fluid,cultured cells, bone marrow sample and/or chorionic villi. Convenientbiological samples may be obtained by, for example, scraping cells fromthe surface of the buccal cavity. The term biological sample includessamples which have been processed to release or otherwise make availablea nucleic acid for detection as described herein. For example, abiological sample may include a cDNA that has been obtained by reversetranscription of RNA from cells in a biological sample. The biologicalsample may be obtained from a stage of life such as a fetus, youngadult, adult, and the like. Fixed or frozen tissues also may be used.Whole blood samples of about 0.5 to 5 ml collected with EDTA, ACD orheparin as anti-coagulant are generally suitable. Amniotic fluid of10-15 ml, cultured cells which are 80-100% confluent in two T-25 flasksand 25 mg of chorionic villi are useful sample amounts for processing.

By “subject” is meant a human or any other animal which contains as CFTRgene that can be amplified using the primers and methods describedherein. A subject can be a patient, which refers to a human presentingto a medical provider for diagnosis or treatment of a disease. A humanincludes pre and post natal forms. Particularly preferred subjects arehumans being tested for the existence of a CF carrier state or diseasestate.

By “identifying” with respect to an amplified sample is meant that thepresence or absence of a particular nucleic acid amplification productis detected. Numerous methods for detecting the results of a nucleicacid amplification method are known to those of skill in the art.

The term “deletion” as used herein encompasses a mutation that removesone or more nucleotides from nucleic acid. Conversely, the term“duplication” refers to a mutation that inserts one or more nucleotidesof identical sequence directly next to this sequence in the nucleicacid. In a preferred embodiment, a deletion or duplication involves asegment of four or more nucleotides.

The term “amplify” as used herein with respect to nucleic acidsequences, refers to methods that increase the representation of apopulation of nucleic acid sequences in a sample. Amplification may beexponential or linear. The sequences amplified in this manner form an“amplicon.” In a preferred embodiment, the amplification by the is bythe polymerase chain reaction (“PCR”) (e.g., Mullis, K. et al., ColdSpring Harbor Symp. Quant. Biol. 51:263-273 (1986); Erlich H. et al.,European Patent Appln. 50,424; European Patent Appln. 84,796, EuropeanPatent Application 258,017, European Patent Appln. 237,362; Mullis, K.,European Patent Appln. 201,184; Mullis K. et al., U.S. Pat. No.4,683,202; Erlich, H., U.S. Pat. No. 4,582,788; and Saiki, R. et al.,U.S. Pat. No. 4,683,194). Other known nucleic acid amplificationprocedures that can be used include, for example, transcription-basedamplification systems or isothermal amplification methods (Malek, L. T.et al., U.S. Pat. No. 5,130,238; Davey, C. et al., European PatentApplication 329,822; Schuster et al., U.S. Pat. No. 5,169,766; Miller,H. I. et al., PCT appln. WO 89/06700; Kwoh, D. et al., Proc. Natl. Acad.Sci. (U.S.A.) 86:1173 (1989); Gingeras, T. R. et al., PCT application WO88/10315; Walker, G. T. et al., Proc. Natl. Acad. Sci, (U.S.A.)89:392-396 (1992)) Amplification may be performed to with relativelysimilar levels of each primer of a primer pair to generate an doublestranded amplicon. However, asymmetric PCR may be used to amplifypredominantly or exclusively a single stranded product as is well knownin the art (e.g., Poddar et al. Molec. And Cell. Probes 14:25-32(2000)). This can be achieved for each pair of primers by reducing theconcentration of one primer significantly relative to the other primerof the pair (e.g. 100 fold difference). Amplification by asymmetric PCRis generally linear. One of ordinary skill in the art would know thatthere are many other useful methods that can be employed to amplifynucleic acid with the invention primers (e.g., isothermal methods,rolling circle methods, etc.), and that such methods may be used eitherin place of, or together with, PCR methods. Persons of ordinary skill inthe art also will readily acknowledge that enzymes and reagentsnecessary for amplifying nucleic acid sequences through the polymerasechain reaction, and techniques and procedures for performing PCR, arewell known. These various amplification methods are merely exemplary.

The phrase “comprise sequence from all or a portion of” in reference toan exon means that the sequence represents all of the exon or at least10 bases of the exon. In other embodiments, most of the exon isamplified, generally greater than 50%, greater than 60%, greater than70%, greater than 80%, greater than 90% and greater than 95%.

The term “specific” as used herein in reference to an oligonucleotideprimer means that the hybridization sequence of the primer has at least12 bases of sequence identity with a portion of the nucleic acid to beamplified when the oligonucleotide and the nucleic acid are aligned. Anoligonucleotide primer that is specific for a nucleic acid is one that,under the appropriate hybridization or washing conditions, is capable ofhybridizing to the target of interest and not substantially hybridizingto nucleic acids which are not of interest. Higher levels of sequenceidentity are preferred and include at least 75%, at least 80%, at least85%, at least 90%, at least 95% and more preferably at least 98%sequence identity.

The term “multiplex PCR” as used herein refers to amplification of twoor more products which are each primed using a distinct primers pair.

The term “hybridize” or “specifically hybridize” as used herein refersto a process where two complementary nucleic acid strands anneal to eachother under appropriately stringent conditions. Hybridizations aretypically and preferably conducted with probe-length nucleic acidmolecules, preferably 20-100 nucleotides in length, more preferably18-50 nucleotides in length. Nucleic acid hybridization techniques arewell known in the art. See, e.g., Sambrook, et al., 1989, MolecularCloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Press,Plainview, N.Y. Those skilled in the art understand how to estimate andadjust the stringency of hybridization conditions such that sequenceshaving at least a desired level of complementary will stably hybridize,while those having lower complementary will not. For examples ofhybridization conditions and parameters, see, e.g., Sambrook, et al.,1989, Molecular Cloning: A Laboratory Manual, Second Edition, ColdSpring Harbor Press, Plainview, N.Y.; Ausubel, F. M. et al. 1994,Current Protocols in Molecular Biology. John Wiley & Sons, Secaucus,N.J.

The term “sense strand” as used herein means the strand ofdouble-stranded DNA (dsDNA) that includes at least a portion of a codingsequence of a functional protein. “Anti-sense strand” means the strandof dsDNA that is the reverse complement of the sense strand.

The term “forward primer” as used herein means a primer that anneals tothe anti-sense strand of dsDNA. A “reverse primer” anneals to thesense-strand of dsDNA.

The term “wildtype” as used herein with respect to the CFTR gene or alocus thereof refers to the CFTR gene sequence which is found in NCBIGenBank locus IDs M58478 (HUMCFTC), AC000111 and AC000061. The cDNA forthe CFTR gene is found in Audrezet et al., Hum. Mutat. (2004) 23 (4),343-357. Alleic variant is one that is “non-disease causing” and reachesa frequency of 1% or more in the population.

The term “familial history” as used herein means the individual hasimmediate family members including parents and siblings. Family historyalso may include grandparents.

Specific primers that aid in the detection of mutant CF genotype aredisclosed. The sequence of substantially pure nucleic acid primers whichare DNA (or an RNA equivalent) and which are useful for amplifying thepromoter region, each of the 27 exons of the CFTR gene, an intronicsequence directly upstream of CFTR exon 9 and various exons of theinternal control target segment are shown in Table 1. The letter F or Rat the end of the primer name indicates whether the primer is a forward(F) or reverse (R) PCR primer. FAM and HEX refer to fluorescentcompounds chemically linked to the 5′ end of the oligonucleotide.

TABLE 1 CFTR Assay Primer Sequences SEQ ID NO Primer Name SequenceHybridizes to: 5 CFDELPF 5′- 6-FAM/ACT GTC GCC CAC CTG CGG -3; promoter6 CFDELPR 5′- CCG CAC ACC ACC CCT TCC -3′ promoter 7 CFDEL1F5′- 6-FAM/AAT TGG AAG CAA ATG ACA TCA CAG -3′ exon 1 8 CFDEL1R5′- TTC CTT TAC CCC AAA CCC AA -3′ intron 1 9 CFDEL2F5′-6-FAM/CCT CTC TTT ATT TTA GCT GGA CCA GAC -3′ intron 1 / axon 2 10CFDEL2R 5′- TCA ACT AAA CAA TGT ACA TGA ACA TAC CT -3′ exon 2 / intron 211 CFDEL3F2 5′-6-FAM/GAA TGG GAT AGA GAG CTG GCT -3′ exon 3 12 CFDEL3R5′- TGT ACA AAT GAG ATC CTT ACC CCT A -3′ exon 3 / intron 3 13 CFDEL4F5′-6-FAM/GAA GTC ACC AAA GCA GTA CAG CC -3′ Exon 4 14 CFDEL4R5′- GCC TGT GCA AGG AAG TAT TAC CT -3′ Exon 4/ Intron 4 15 CFDEL5F5′-6-FAM/TTT AGA CTT TAA AGC TGT CAA GCC G -3′ Intron 4 /. Exon 5 16CFDEL5R 5′- CCG CCT TTC CAG TTG TAT AAT TTA T -3′ Intron 5 17 CFDEL6aF5′-6-FAM/GGA CTT GCA TTG GCA CAT TT -3′ Exon 6a 18 CFDEL6aR5′- TGC TAC CTG TAC TTC ATC ATC ATT C -3′ Exon 6a / Intron 6a 19CFDEL6bF 5′-6-FAM/TGT AAA ACG ACG GCC AGT AGA TCA GAG Exon 6bAGC TGG GAA GAT CA -3′ 20 CFDEL6bR5′- GGT GGA AGT CTA CCA TGA TAA ACAT -3′ Intron 6b 21 CFDEL7F5′-6-FAM/AAC AGA ACT GAA ACT GAC TCG GA -3′ Exon 7 22 CFDEL7R5′- GCA GCA TTA TGG TAC ATT ACC TGT A -3′ Exon 7 / Intron 7 23CFDELEX8F2 5′-6-FAM/TTT TTT TTT TTT TTT ATA AGA TGT AGC ACA Intron 7ATG AGA GTA TAA AGT -3′ 24 CFDEL8R 5′- TAA AAA TTC TGA CCT CCT CCC A -3′exon 8 / intron 8 25 CFDELex9F2 5′-6-FAM/TGG ATC ATG GGC CAT GTG C -3′Intron 8 26 CFDEL9R 5′- CAA AAG AAC TAC CTT GCC TGC T -3′ intron 9 27CFDEL10F 5′-6-FAM/TCC AGA CTT CAC TTC TAA TGG TGA -3′ Intron 9 / exon 1028 CFDEL10R 5′- GTG AAG GGT TCA TAT GCA TAA TCA A -3′ intron 10 29CFDEL11F 5′-6-FAM/AGG ACA TCT CCA AGT TTG CAG A -3′ intron 10 /exon 1130 CFDEL11R 5′- GCA AAT GCT TGC TAG ACC AAT AAT T -3′ intron 11 31CFDEL12F 5′-6-FAM/TGA CCA GGA AAT AGA GAG GAA ATG -3′ intron 11 32CFDEL12R 5′- CTA TGA TGG GAC AGT CTG TCT TTC T -3′ intron 12 33 CFDEL13F5′-6-FAM/GTG ATC AGC ACT GGC CCC AC -3′ Exon 13 34 CFDEL13R5′- CCC CCA AGC GAT GTA TAC CT -3′ Intron 13 35 CFDEL14aF5′-6-FAM/TTT TGA GTG CTT TTT TGA TGA TAT GGA GA -3′ Exon 14a 36CFDEL14aR 5′- AAC ATT CTT ACC TCT GCC AGA AAA -3′ Exon 14a /intron 14a37 CFDEL14bF 5′-6-FAM/GGA GGA ATA GGT GAA GAT GTT AGA A -3′ Intron 14a38 CFDEL14bR 5′- GGA GAA ATG AAA CAA AGT GGA TTA C -3′ Intron 14b 39CFDELI5F 5′-6-FAM/TTT TTT TTC ACT CCT CTT CAA GAC AAA Exon 15 GGG -3′ 40CFDEL15R 5′- TAC CTG CTT TCA ACG TGT TGA G -3′ Exon 15 / Intron 15 41CFDEL16F 5′-6-FAM/GCG TCT ACT GTG ATC CAA ACT TAG T -3′ Intron 15 42CFDEL16R 5′- GGA CTT CAA CCC TCA ATC AAA TAA A -3′ Intron 16 43CFDEL17aF 5′- 6-FAM/TTC TCA CCA ACA TGT TTT CTT TGA TC -3′ Intron 16 44CFDEL17aR 5′- GTC ATA CCT TCA GAT TCC AGT TGT T -3′Exon 17a / Intron 17a 45 CFDEL17bF25′-6-FAM/TGG AAA TAT TTC ACA GGC AGG AGT C -3′ intron 17a /exon 17b 46CFDEL17BR2 5′- CAT TTT ATT CAT TGA AAA TTT TTT ACT TAA ATG -3′intron 17b 47 CFDEL18F2 5′-6-FAM/TAC TTA CTA TAT GCA GAG CAT TAT TCT ATTIntron 17b AGT AG -3′ 48 CFDEL18R5′- CTT ACC AAG CTA TCC ACA TCT ATG C -3′ Exon 18 / Intron 18 49CFDEL19F 5′-6-FAM/ATG CGA TCT GTG AGC CGA GT -3′ Exon 19 50 CFDEL19R5′- CCC TCT GGC CAG GAC TTA TT -3′ Exon 19 / Intron 19 51 CFDEL20F5′-6-FAM/GTG GGC CTC TTG GGA AGA AC -3′ Exon 20 52 CFDEL20R5′- GCT CAC CTG TGG TAT CAC TCC AA -3′ Exon 20 / Intron 20 53 CFDEL21F5′-6-FAM/TGT AAA ACG ACG GCC AGT CTT TTC TTT TTT intron 20/ exon 21GCT ATA GAA AGT ATT TAT TTT -3′ 54 CFDEL21R5′- CAG CCT TAC CTC ATC TGC AAC TT -3′ exon 21 / intron 21 55 CFDEL22F5′-6-FAM/GTT GGG CTC AGA TCT GTG ATA GA -3′ exon 22 56 CFDEL22R5′- CAC ACT GGA TCC AAA TGA GCA C -3′ exon 22 /intron 22 57 CFDEL23F5′-6-FAM/CAT TAC TGT TCT GTG ATA TTA TGT GTG GTA -3′ intron 22 58CFDEL23R 5′- CAA GGG CAA TGA GAT CTT AAG TAA -3′ intron 23 59 CFDEL24F5′-6-FAM/AGA AGA GAA CAA AGT GCG GCA -3′ Exon 24 60 CFDEL24R5′- TGT ATC TTG CAC CTC TTC TTC TGT C -3′ Exon 24 61 Upex9F5′- /5HEX/TTT TTT TTT TTG TAA AAC GAC GGC CAG Intron 8TTT CAG TCT TTA CTG AAA TTA AAA AAT CTT -3′ 62 Upex9R5′- ATA GCA TAC GGT TTC TAG AGG ACA TG -3′ Intron 8 63 F5F 5′- HEX/TTG AAG GAA ATG CCC CAT TAT TTA GCC AGG - Intron 11 3′ 64 F5R 5′- TGC TTA ACA AGA CCA TAC TAC AGT GAC GT - 3′ Exon 10 65 F2F 5′- 6-FAM/AGG AGG ACC TGT CCT CCC AGA TGG T -3′ Sequence Upstreamof exon 1 66 F2R 5′ - CTG TCC AGC CAG GAG ACC CCA -3′ Intron 1 67 TSF 5′- HEX/CAT TCT TAC CTG GTC CCC AGG ACA AAG -3′ Exon 7 / Intron 8 68 TSR5′ - GTC CTA CAA CCC TGT CAC CCA CAT C -3′ Exon 7

Various subsets of the primer pairs from Table 1 may be used in amultiplex PCR. For example, primer sequences can be used to verify asuspected CFTR promoter deletion or duplication and to asses the extentof such deletion or duplication. Primer pairs which can be used toamplify three regions upstream from the promoter (Table 3) designated asUPr1, UPr2 and UPr3, are shown in Table 2. These may be combined in amultiplex amplification with primer pairs for CFTR exons 1, 2, 3 and 4and/or others. In addition, one may include any number of internalcontrol primer pairs.

TABLE 2 CFTR promoter and internal control primerconcentrations in Master Mix SEQ ID Primer NO: Name Primer Sequence 69UpPr1F FAM-5′- GAA TTC AAA GGA AAA CAT AAG ATG CAA TTC -3′ 70 UpPr1R5′- AAC ACA CAT TAC ACT CTT ACA AAG ATG TTT -3′ 71 UpPr2F1 FAM-5′- CCA CAC TAA CAG TTA TAA ACC AAA CAA CA -3′ 72 UpPr2R 5′- CAC CAG GAA AGA ATT TCA GCA TTT -3′ 73 UpPr3F FAM-5′- CTA AAA CAC TCC AAA GCC TTC CTT -3′ 74 UpPr3R 5′- TTC AGG TTT AGG TGA GTG AAC TCC AA- 3′

Amplified target segments can be efficiently evaluated by size and/ordetectable moiety using commercially available automated systems. Forexample, ABI PRISM® 3100 Genetic Analyzer can be used with an ABI PRISM3100 capillary array, 36-cm (P/N#4315931). This provides a multi-colorfluorescence-based DNA analysis system that uses capillaryelectrophoresis (CE) with 16 capillaries operating in parallel toseparate labeled PCR products. A CE DNA sequencer/analyzer that operates96 capillaries may be preferable in assays wherein 96-well plates areused. Analyzers with the capacity to process 96 wells include theMegaBACE™ 1000 DNA Analysis System (Molecular Dynamics, Inc and AmershamPharmacia Biotech) and the 3700 DNA Analyzer from (Perkin-ElmerBiosystems).

The primers in Table 1 and 2 are useful for diagnosing a genetic basisfor cystic fibrosis (CF) by analyzing a sample comprising nucleic acidsfrom an individual. The method includes determining if the promoterregion of the CFTR gene contains deleted or duplicated sequenceinvolving four or more nucleotides, wherein the promoter regionrepresents 250 nucleotides or more directly upstream of the CFTR startcodon. These promoter/exon mutations include a deletion in a segment ofthe CFTR promoter region including the adjoining CFTR exon 1 or adeletion in a segment of the CFTR promoter region including theadjoining CFTR exons 1 and 2. The deletion involving the promoter regionand exon 1 comprises at least 1,800 nucleotides in length of which atleast 1,630 nucleotides represents sequence from the CFTR promoterregion. The deletion involving the promoter and exons 1 and 2 comprisesat least 28,000 nucleotides in length of which at least 3,570nucleotides represents sequence from the CFTR promoter region. Thesedeletions may be detected using the methods disclosed herein or othermethods of deletion detection well known in the art.

Another method for detecting CF mutations is SQF PCR (i.e.,semi-quantitative fluorescent multiplex PCR). This method also may bereferred to as QMPSF (quantitative multiplex PCR of short fragments).See Bombieri et al, Eur J Human Genetics 13(5):687-9 (May 2005). Arelated approach is described by Yau and co-workers (Yau, S. C., et al.,1996, J. Med. Genet. 33:550-8). The principle of the method rests oncomparisons of the fluorescent profiles of multiplex PCR fragmentsobtained from different samples, the amplification being stopped at theexponential phase. This procedure allows the detection of heterozygousdeletions (i.e., approximately twofold reduction of fluoroescenceintensity) and heterozygous duplications (i.e., approximately 1.5-foldincrease in fluoroescence intensity). SQF PCR for simultaneous detectionof deletions or duplications involving any of the 27 exons and thepromoter of the CFTR gene is described in U.S. patent application Ser.No. 11/074,903 titled “Cystic Fibrosis Gene Mutations” and filed Mar. 7,2005. Fragments representing any of the 27 CFTR exons can be amplifiedusing the primers of Table 1 and operational protocols known to those ofskill in the art. At the end of PCR cycling, the fluorescent PCRproducts are heat denatured, chilled on ice, and separated on amulti-capillary sequencer, e.g., ABI PRISM 3100 from Applied Biosystems.The resulting electropherograms are analyzed (manufacturer's Genescansoftware) to provide identification of product by size and to obtaincorrelated fluorescence intensity.

In the context of the exon 6b-10 duplication, one can use primers fromTable 1 to (a) amplify sequence from one or more of exon 6b, 7, 8, 9,and 10 from nucleic acid from an individual; (b) identify the amplifiedexon sequence; and (c) compare the amount of each amplified exonsequence versus that for a normal CFTR gene, wherein a substantialincrease in the amount of amplified exon sequence observed versus thatfor a normal CFTR gene indicates a duplication of exon 6b-10. In thisapproach, amplification is conducted in the linear phase in accordancewith SQF PCR. Sequence representing exons may be amplified using primersfor one or more introns within the duplicated 6b-10 segment and comparedto that similarly amplified from a normal gene. Sequence also may beamplified from introns instead of or in addition to sequence beingamplified from exons. If multiplex amplification is used, one primer ofeach primer pair may be detectably labeled to allow discrimination ofthe different amplified products.

An additional method of identifying CF mutations is MLPA (i.e.,multiplex ligation-dependent probe amplification.). As known by those ofskill in the art, MLPA is a sensitive technique enabling relativequantification of up to about 40 different nucleic acid sequences in onereaction (Schouten, J. P., et al., 2002, Nucleic Acid Research 30:e57;Sellner and Taylor, 2004 Human Mutation 23: 413-419). The method isbased on adjacent hybridizing probes that if properly are hybridized,can be ligated together and then amplified using a specific primer pair.If a mutation is present, then a different adjoining probe willhybridize, be ligated and then amplified. The size of the amplifiedproduct will reveal the identify of the ligated probes. The amplifiedproducts also may be discriminated using size and/or differentiallabeling (e.g. different fluorescent molecules).

In the present context, appropriate probes and primers can be readilydesigned for detecting the 6b-10 duplication described herein or fordetecting other CFTR deletions or duplications. For example, the twoadjoining probes for the normal CFTR allele would be designed tohybridize so that ligation would occur between IVS10+2197 andIVS10+2198. In the case of the 6b-10 duplicated allele, the twoadjoining probes would be designed to hybridize so that ligation wouldoccur between IVS10+2197 and IVS6a+415.

A further method of identifying CF mutations is MAPH (i.e., multiplexamplifiable probe hybridization). See generally White et al. 2002, Amer.J. Human Genetics, 71:365-374; Sellner and Taylor, 2004. Human Mutation.23: 413-419. As known by those of skill in the art, MAPH is based on aquantitative PCR of short DNA probes recovered after hybridization to atarget of interest in immobilized genomic DNA. The target of interest iscloned into a vector and the probes are made by PCR using primers thatflank the target sequence in the vector. In this way, the generatedprimers can have a known 5′ primer site for subsequent PCR. The probesthat hybridize to genomic DNA following appropriate stringent washingare removed and their identity determined by PCR using primers to the 5′primer sites. A universal 5′ primer site can be incorporated into bothforward and reverse primers along with appropriate stuffer sequence toobtain multiplex amplification of the bound probe and discrimination ofamplicans by size. Probes directed to portions of the various exons ofthe CFTR gene are useful for MAPH. Duplications or deletions in genomicDNA show up as more or less probe binding, respectively in the MAPHmethod. Thus, typical CFTR exon probes for any or all of exon 6b, 7, 8,9 and 10 can be used for detecting the 6b-10 CFTR exon duplication. Onecan also design a specific probe for MAPH by that spans the junction offusion of IVs 10 to IVS6a.

An additional method of identifying CF mutations is long range PCR,which as known by those of skill in the art allows the amplification ofPCR products which are much larger than those achieved with conventionalTaq polymerases. In this regard, the present invention contemplates useof primers that flank the duplicated segment. Examples of such primersthat flank the duplicated segment include any sequence precedingIVS6a+415 and any primer sequence which follows IVS10+2987. Suchanalysis of wild-type CFTR gene will amplify a product that includes26,817 bp while a duplication of exons 6a through 10 in one allele willresult in two fragments, one of which includes the 26,817 representingthe single 6b-10 segment and a fragment including 53,634 bp whichincludes the double version of 6b-10. By placing the primers close toIVS6a+415 and IVS10+2987, the resulting amplified products will approachthe size of the target 6b-10 segment (26,817 bp) and 6b-10-6b′-10′(54,634 bp).

Yet another method of identifying CF mutations is junction PCR. In thecontext of the exon 6b-10 duplication, primers are employed that flankthe fusion of intron 10 and intron 6a in the mutant allele. Primers forthis purpose, design of which is understood by those of skill in theart, would complement CFTR DNA upstream from IVS10+2987 (forward primer)and downstream of IVA6a+415 (reverse primer). The amplification of thejunction encompassed by the primer would be confirmation of duplication,and DNA sequencing of the amplified junction fragment may be used toshow the duplication junction. Restriction digestion of the amplifiedjunction fragment using the enzyme ApaI or others that recognize thejunction fragment can also be used as a confirmation.

An additional method of identifying CF mutations is RealTime PCR. In thecontext of the exon 6b-10 duplication, primers can be used that flankthe intron 10/intron 6a junction of the mutant sequence are easilydesigned by those of skill in the art, are employed to amplify anddetect the junction on a realtime instruction, e.g., the AppliedBiosystems 7900, using TaqMan probes or equivalents.

In an additional method of identification of CFTR mutations includingthe exon 6b-10 duplication is Southern Blot analysis, well known tothose of skill in the art. In this method, DNA is digested intofragments, preferably with a restriction endonuclease and the fragmentsseparated by size via gel electrophoresis using, for example, agarose asthe medium. To the developed DNA laden gel is pressed a nitrocelluloseor nylon membrane to which the DNA sticks. The transferred DNA is thenpermanently fixed to the membrane by any of several methods, includingfor example, exposure to ultraviolet light or heat. The identity of thetransferred DNA fragments is then determined by probing withcomplementary DNA probes which are labeled by any of several strategiesincluding, for example, radioactivity, chromophoric, fluorophoric, orspecific ligand including, for example, biotinylation. Visualization ofprobe bound to complementary DNA affixed to the membrane can occur basedon the labeling method of the probe; for example, X-ray photographicexposure can revealed radioactive labeled probe, and fluoroescentlabeling can be revealed by illumination with an exciting source andobservation of the corresponding emitted signal. In application todetection of the CFTR 6b-10 duplication, enzymes that digest DNA outsideexons 6b-10 can be used to detect the native 6b-10 segment (26,817 bp)and the duplicated segment 6b-10-6b′-10′ (53,634 bp). In anotherapplication, digestion of the DNA with restriction enzymes (e.g. ApaI)that identify the junction fragment can help in identifying the exon6b-10 duplication.

In a further method of identification of the CFTR 6b-10 exonduplication, the unique protein sequence that occurs as a result of theduplication may be detected. In a preferred approach, antibodies thatspecifically react with the unique protein segment are used to detectthe 6b-10 duplication. For example, in the case of Dup ex 6b-10, thereis an out-of-frame addition of 8 amino acids after codon E528 of Exon10, encoding a new C-terminal sequence between 529 and 536(Arg-Ser-Glu-Ser-Trp-Glu-Asp-Glu; SEQ ID NO: 1). Antibody bindingspecifically to a truncated CFTR protein via its unique C terminalsegment such as that of SEQ ID NO:1 may be detected by any methods knownin the art, including, for example, ELISA, radioimmunoassay, and westernblotting.

J Antibodies may be detectably labeled by methods known in the art.Labels include, but are not limited to, radioisotopes such as ¹²⁵I,enzymes (e.g., peroxidase, alkaline phosphatase, beta-galactosidase, andglucose oxidase), enzyme substrates, luminescent substances, fluorescentsubstances, biotin, and colored substances. In binding these labelingagents to the antibody, the maleimide method (J. Biochem. (1976), 79,233), the activated biotin method (J. Am. Chem. Soc. (1978), 100, 3585)or the hydrophobic bond method, for instance, can be used.

One can detect the duplication by using also antibodies that recognizeregions of the CFTR protein up to the junction (i.e. E528), such thatthe truncated protein will display a molecular weight different from thefull length normal CFTR protein.

One skilled in the art would readily recognize that the measurement ofSEQ ID NO:1 or other unique C-terminal CFTR sequence can be in an ELISAwhich requires a specific antibody to the unique amino acid sequence,which antibody is readily available using standard methods known in theart. In the Western blot method, a protein mixture potentiallycontaining the CFTR product with unique C-terminal amino acid sequence(e.g. SEQ ID NO:1) is subjected to gel electrophoresis, usually underdenaturing conditions. The developed gel is then blotted withnitrocellulose paper to which the proteins in the gel adhere,maintaining relative positioning. The membrane is then blocked by beingflooded with a protein solution, for example bovine serum albumin, inorder to prevent non-specific protein interactions between the membraneand the antibody protein. The blocked nitrocellulose membrane is thenincubated with a first (i.e., “primary”) directed to the peptide ofinterest, for example SEQ ID NO: 1. After rinsing to remove unboundprimary antibody, a secondary antibody, directed to the primaryantibody, is introduced. The secondary antibody can be linked to anenzyme that can allow for visualization as, for example, by havingspecificity for a non-chromophoric substrate which turns colored afterreaction with the enzyme linked to the secondary antibody. Othervisualization methods known in the art include, without limitation,radioactivity and fluoroscence.

The term “antibody” refers to a protein consisting of one or morepolypeptides substantially encoded by immunoglobulin genes or fragmentsof immunoglobulin genes. The recognized immunoglobulin genes include thekappa, lambda, alpha, gamma, delta, epsilon and mu constant regiongenes, as well as myriad immunoglobulin variable region genes. Lightchains are classified as either kappa or lambda. Heavy chains areclassified as gamma, mu, alpha, delta, or epsilon, which in turn definethe immunoglobulin classes, IgG, IgM, IgA, IgD and IgE, respectively. Atypical immunoglobulin (antibody) structural unit is known to comprise atetramer. Each tetramer is composed of two identical pairs ofpolypeptide chains, each pair having one “light” (about 25 kD) and one“heavy” chain (about 50-70 kD). The N-terminus of each chain defines avariable region of about 100 to 110 or more amino acids primarilyresponsible for antigen recognition. The terms variable light chain (VL)and variable heavy chain (VH) refer to these light and heavy chainsrespectively. An antibody can be specific for a particular antigen. Theantibody or its antigen can be either an analyte or a binding partner.Antibodies exist as intact immunoglobulins or as a number ofwell-characterized fragments produced by digestion with variouspeptidases. Thus, for example, pepsin digests an antibody below thedisulfide linkages in the hinge region to produce F(ab)′2, a dimer ofFab which itself is a light chain joined to VH-CH1 by a disulfide bond.The F(ab)′2 may be reduced under mild conditions to break the disulfidelinkage in the hinge region thereby converting the (Fab′)2 dimer into anFab′ monomer. The Fab′ monomer is essentially an Fab with part of thehinge region (see, Fundamental Immunology, W. E. Paul, ed., Raven Press,N.Y. (1993), for a more detailed description of other antibodyfragments). While various antibody fragments are defined in terms of thedigestion of an intact antibody, one of skill will appreciate that suchFab′ fragments may be synthesized de novo either chemically or byutilizing recombinant DNA methodology. Thus, the term antibody, as usedherein also includes antibody fragments either produced by themodification of whole antibodies or synthesized de novo usingrecombinant DNA methodologies. Preferred antibodies include single chainantibodies, more preferably single chain Fv (scFv) antibodies in which avariable heavy and a variable light chain are joined together (directlyor through a peptide linker) to form a continuous polypeptide. A singlechain Fv (“scFv”) polypeptide is a covalently linked VH::VL heterodimerwhich may be expressed from a nucleic acid including VH- and VL-encodingsequences either joined directly or joined by a peptide-encoding linker.Huston, et al. (1988) Proc. Nat. Acad. Sci. USA, 85:5879-5883. A numberof structures for converting the naturally aggregated—but chemicallyseparated light and heavy polypeptide chains from an antibody V regioninto an scFv molecule which will fold into a three dimensional structuresubstantially similar to the structure of an antigen-binding site. See,e.g. U.S. Pat. Nos. 5,091,513 and 5,132,405 and 4,956,778.

Other CF mutations that can be detected together with the detection ofthe exon 6b-10 duplication include those known under symbols: 2789+5G>A;711+1G>T; W1282X; 3120+1G>A; d1507; dF508; (F508C, 1507V, 1506V);N1303K; G542X, G551D, R553X, R560T, 1717-1G>A: R334W, R347P, 1078delT;R117H, 1148T, 621+1G>T; G85E; R1162X, 3659delC; 2184delA; A455E, (5T,7T, 9T); 3849+10kbC>T; and 1898+1G>A, are described in U.S. patentapplication Ser. No. 396,894, filed Apr. 22, 1989, application SerialNo. 399,945, filed Aug. 29, 1989, application Serial No. 401,609 filedAug. 31, 1989. and U.S. Pat. Nos. 6,011,588 and 5,981,178, which arehereby incorporated by reference in their entirety.

Still other CFTR mutations and PCR primer pairs for amplifying segmentsof the CFTR gene containing the mutations are shown in Table 3.

TABLE 3 CF mutations and associated amplification primers CF Forward andReverse Mutation Nucleotide Change PCR Primers S158T 605G−>C q4e1F andq4e1R V358I 1204G−>A q7e3F and q7e4R 119del6 1198-1202del (deletesTGGGCT q7e3F and q7e4R and results in W356 and A357) G451V 1484G−>Tq9e9F and q9e11R K481E 1573A−>G s10e3F and s10e2R C491S 1064G−>C s10e3Fand s10e2R K503N + 1641-1642AG−>T (deletes s10e3F and s10e2R frameshift1641A and 1642G and replaces with T) 2949del5 2949-2953del (deletesTACTC) q15e3F and q15e4R H949L 2798A−>T q15e3F and q15e4R T1036N3239C−>A q17ae1F and q17ae1R F1099L 3429C−>A q17be1F and q17be1R

The primers for amplifying segments of the CFTR gene may hybridize tocoding or non-coding CFTR sequences under stringent conditions.Preferred primers are those that flank mutant CF sequences. Primers forCF mutations in Table 3 are shown in Table 4.

TABLE 4 Amplification primer sequences for CF mutations CF MutationForward and Reverse PCR Primers S158T q4e1F: (SEQ ID NO: 75)TGTAAAACGACGGCCAGTaaagtettgtgttgaaattct cagg q4e1R: (SEQ ID NO: 76)CAGGAAACAGCTATGACCCAGCTCACTACCTAATTTATG ACAT V358Iq7e3F: (SEQ ID NO: 77) 119del6 TGTAAAACGACGGCCAGTcttccattccaagatcccq7e4R: (SEQ ID NO: 78) CAGGAAACAGCTATGACCGCAAAGTTCATTAGAACTGATC G451Vg9e9F: (SEQ ID NO: 79) TGTAAAACGACGGCCAGTtggatcatgggccatgtgc andg9e11R: (SEQ ID NO: 80) CAGGAAACAGCTATGACCAAAGAGACATGGACACCAAAT TAAGK481E s10e3F: (SEQ ID NO: 81) C491STGTAAAACGACGGCCAGTagcagagtacctgaaacagga K503N + s10e2R: (SEQ ID NO: 82)frame- CAGGAAACAGCTATGACCCATTCACAGTAGCTTACCCA shift 2949de15q15e3F: (SEQ ID NO: 83) TGTAAAACGACGGCCAGTggttaagggtgcatgctatc H949Lq15e4R: (SEQ ID NO: 84) CAGGAAACAGCTATGACCGGCCCTATTGATGGTGGATC T1036Nq17ae1F: (SEQ ID NO: 85) TGTAAAACGACGGCCAGTacactttgtccactttgcq17ae1R: (SEQ ID NO: 86) CAGGAAACAGCTATGACCAGATGAGTATCGCACATTC F1099Lq17be1F: (SEQ ID NO: 87) TGTAAAACGACGGCCAGTatctattcaaagaatggcacq17be1R: (SEQ ID NO: 88) CAGGAAACAGCTATGACCGATAACCTATAGAATGCAGC

CF mutations in the amplified nucleic acid may be identified in any of avariety of ways well known to those of ordinary skill in the art. Forexample, if an amplification product is of a characteristic size, theproduct may be detected by examination of an electrophoretic gel for aband at a precise location. In another embodiment, probe molecules thathybridize to the mutant or wildtype CF sequences can be used fordetecting such sequences in the amplified product by solution phase or,more preferably, solid phase hybridization. Solid phase hybridizationcan be achieved, for example, by attaching the CF probes to a microchip.Probes for detecting CF mutant sequences are well known in the art. SeeWall et al. “A 31-mutation assay for cystic fibrosis testing in theclinical molecular diagnostics laboratory,” Human Mutation, 1995;5(4):333-8, which specifies probes for CF mutations ΔF508 (exon 1),G542X (exon 11), G551D (exon 11), R117H (exon 4), W1282X (exon 20),N1303K (exon 21), 3905insT (exon 20), 3849+10Kb (intron 19), G85E (exon3), R334W (exon 7), A455E (exon 9), 1898+1 (exon 12), 2184delA (exon13), 71 1+1 (exon 5), 2789+5 (exon 14b), Y1092x exon 17b), ΔI507 (exon10), S549R(T-G) (exon 11), 621+1 (exon 4), R1162X (exon 19), 1717-1(exon 11), 3659delC (exon 19), R560T (exon 11), 3849+4(A-G) (exon 19),Y122X (exon 4), R553X (exon 11), R347P (exon 7), R347H (exon 7), Q493X(exon 10), V520F (exon 10), and S549N (exon 11).

CF probes for detecting mutations as described herein may be attached toa solid phase in the form of an array as is well known in the art (see,U.S. Pat. Nos. 6,403,320 and 6,406,844). For example, the fullcomplement of 24 probes for CF mutations with additional control probes(30 in total) can be conjugated to a silicon chip essentially asdescribed by Jenison et al., Biosens Bioelectron. 16(9-12):757-63 (2001)(see also U.S. Pat. Nos. 6,355,429 and 5,955,377). Amplicons thathybridized to particular probes on the chip can be identified bytransformation into molecular thin films. This can be achieved bycontacting the chip with an anti-biotin antibody or streptavidinconjugated to an enzyme such as horseradish peroxidase. Followingbinding of the antibody (or streptavidin)-enzyme conjugate to the chip,and washing away excess unbound conjugate, a substrate can be added suchas tetramethylbenzidine (TMB) {3,3′,5,5′Tetramethylbenzidinc} to achievelocalized deposition (at the site of bound antibody) of a chemicalprecipitate as a thin film on the surface of the chip. Otherenzyme/substrate systems that can be used are well known in the art andinclude, for example, the enzyme alkaline phosphatase and5-bromo-4-chloro-3-indolyl phosphate as the substrate. The presence ofdeposited substrate on the chip at the locations in the array whereprobes are attached can be read by an optical scanner. U.S. Pat. Nos.6,355,429 and 5,955,377, which are hereby incorporated by reference intheir entirety including all charts and drawings, describe preferreddevices for performing the methods of the present invention and theirpreparation, and describes methods for using them.

The binding of amplified nucleic acid to the probes on the solid phasefollowing hybridization may be measured by methods well known in the artincluding, for example, optical detection methods described in U.S. Pat.No. 6,355,429. In preferred embodiments, an array platform (see, e.g.,U.S. Pat. No. 6,288,220) can be used to perform the methods of thepresent invention, so that multiple mutant DNA sequences can be screenedsimultaneously. The array is preferably made of silicon, but can beother substances such as glass, metals, or other suitable material, towhich one or more capture probes are attached. In preferred embodiments,at least one capture probe for each possible amplified product isattached to an array. Preferably an array contains 10, more preferably20, even more preferably 30, and most preferably at least 60 differentcapture probes covalently attached to the array, each capture probehybridizing to a different CF mutant sequence. Nucleic acid probesuseful as positive and negative controls also may be included on thesolid phase or used as controls for solution phase hybridization.

Another approach, variously referred to as PCR amplification of specificallele (PASA) (Sarkar, et al., 1990 Anal. Biochem. 186:64-68),allele-specific amplification (ASA) (Okayama, et al., 1989 J. Lab. Clin.Med. 114:105-113), allele-specific PCR (ASPCR) (Wu, et al. 1989 Proc.Natl. Acad. Sci. USA. 86:2757-2760), and amplification-refractorymutation system (ARMS) (Newton, et al., 1989 Nucleic Acids Res.17:2503-2516). The method is applicable for single base substitutions aswell as micro deletions/insertions. In general, two complementaryreactions are used. One contains a primer specific for the normal alleleand the other reaction contains a primer for the mutant allele (bothhave a common 2nd primer). One PCR primer perfectly matches one allelicvariant of the target, but is mismatched to the other. The mismatch islocated at/near the 3′ end of the primer leading to preferentialamplification of the perfectly matched allele. Genotyping is based onwhether there is amplification in one or in both reactions. A band inthe normal reaction only indicates a normal allele. A band in the mutantreaction only indicates a mutant allele. Bands in both reactionsindicate a heterozygote. As used herein, this approach will be referredto as “allele specific amplification (ASA).”

Allele specific amplification can be used to detect the exons 6b through10 duplication by using as the ASA primer, one that hybridizes partiallyacross the junction. The extent of junction overlap can be varied toallow specific amplification. For example, most of the forward primersequence is designed to hybridize upstream of the junction site withonly a few nucleotides hybridizing on the downside of the junction site.One skilled in the art can establish conditions where such primerhybridizes specifically to the junction fragment. The ASA primer may bedesigned to hybridize to the forward or reverse strand. Amplification isachieved using a primer down stream of the ASA primer. This primer setwill be able to amplify a fragment from nucleic acid containing the 6bthrough 10 duplication but not from normal DNA. This approach can beused independently of any other amplification or as a secondary stepafter long range amplification or junction amplification.

In yet another approach for detecting wildtype or mutant CF sequences inamplified DNA is single nucleotide primer extension or “SNuPE.” SNuPEcan be performed as described in U.S. Pat. No. 5,888,819 to Goelet etal., U.S. Pat. No. 5,846,710 to Bajaj, Piggee, C. et al. Journal ofChromatography A 781 (1997), p. 367-375 (“Capillary Electrophoresis forthe Detection of Known Point Mutations by Single-Nucleotide PrimerExtension and Laser-Induced Fluorescence Detection”); Hoogendoorn, B. etal., Human Genetics (1999) 104:89-93, (“Genotyping Single NucleotidePolymorphism by Primer Extension and High Performance LiquidChromatography”); and U.S. Pat. No. 5,885,775 to Haff et al. (analysisof single nucleotide polymorphism analysis by mass spectrometry). InSNuPE, one may use as primers such as those specified in Table 4.

Another method for detecting CF mutations includes the Luminex xMAPsystem which has been adapted for cystic fibrosis mutation detection byTM Bioscience and is sold commercially as a universal bead array(Tag-It™).

Still another approach for detecting wildtype or mutant CF sequences inamplified DNA is oligonucleotide ligation assay or “OLA” or “OL”. TheOLA uses two oligonucleotides which are designed to be capable ofhybridizing to abutting sequences of a single strand of a targetmolecules. One of the oligonucleotides is biotinylated, and the other isdetectably labeled. If the precise complementary sequence is found in atarget molecule, the oligonucleotides will hybridize such that theirtermini abut, and create a ligation substrate that can be captured anddetected. See e.g., Nickerson et al. (1990) Proc. Natl. Acad. Sci.U.S.A. 87:8923-8927, Landegren, U. et al. (1988) Science 241:1077-1080and U.S. Pat. No. 4,998,617.

These above approaches for detecting wildtype or mutant CF sequence inthe amplified nucleic acid is not meant to be limiting, and those ofskill in the art will understand that numerous methods are known fordetermining the presence or absence of a particular nucleic acidamplification product.

Multiplex amplification as described herein may include primers foramplifying one or more non-CFTR gene segments as an internal control.Such internal controls may include exon 1 of the coagulation factor 2gene of chromosome 11 (“F2”), exon 10 of coagulation factor V ofchromosome 11 (“F5”) and/or exon 7 of the Tay Sachs HEXA gene ofchromosome 15 (“TS”). In a preferred embodiment, all three of theseexons may be amplified. Thus, the method can evaluate by a singlemultiplex PCR, a total of at least 32 target segments, the segmentsrepresenting 27 exons of the CFTR gene, the CFTR promoter region, UpEx9and three internal control exons.

To assist in identifying amplified segments, at least one primer fromsome or all of the primer pairs in the multiplex can be labeled with adetectable moiety. It would be evident to the skilled artisan that thedetectable moiety could be attached in any manner of variety that doesnot interfere with the oligonucleotide to function as an amplificationprimer.

The phrase “detectable moiety” is used herein to denote any molecule (orcombinations of molecules) that may be attached or otherwise associatedwith a molecule so that the molecule can be detected indirectly bydetecting the detectable moiety. A detectable moiety can be aradioisotope (e.g., iodine, indium, sulfur, hydrogen etc.) a dye orfluorophor (e.g., cyanine, fluorescein, rhodamine), protein (e.g.,avidin, antibody), enzyme (peroxidase, phosphatase, etc.), or any otheragent that can be detected directly or indirectly. An enzyme is anexample of a detectable moiety detected by indirect means. In this case,the enzyme is attached to the target nucleic acid and the presence ofthe enzyme is detected by adding an appropriate substrate that whenacted upon by the enzyme, causes the substrate to change in color or torelease a cleavage product that provides a different color from theoriginal substrate.

The term “fluorescent detectable moiety” or “fluorophore” as used hereinrefers to a molecule that absorbs light at a particular wavelength(excitation frequency) and subsequently emits light of a longerwavelength (emission frequency). A fluorescent detectable moiety can bestimulated by a laser with the emitted light captured by a detector. Thedetector can be a charge-coupled device (CCD) or a confocal microscope,which records its intensity.

A useful detectable moiety is a cyanine dye such as Cy-5 and Cy-3, FAM,HEX, and the like. A detectable moiety may include more than onechemical entity such as in fluorescent resonance energy transfer (FRET).Resonance transfer results an overall enhancement of the emissionintensity. For instance, see Ju et. al. (1995) Proc. Nat'l Acad. Sci.(USA) 92: 4347. To achieve resonance energy transfer, the firstfluorescent molecule (the “donor” fluor) absorbs light and transfers itthrough the resonance of excited electrons to the second fluorescentmolecule (the “acceptor” fluor). In one approach, both the donor andacceptor dyes can be linked together and attached to the oligo primer.Methods to link donor and acceptor dyes to a nucleic acid have beendescribed previously, for example, in U.S. Pat. No. 5,945,526 to Lee etal. Donor/acceptor pairs of dyes that can be used include, for example,fluorescein/tetramethylrohdamine, IAEDANS/fluroescein, EDANS/DABCYL,fluorescein/fluorescein, BODIPY FL/BODIPY FL, and Fluorescein/QSY 7 dye.See, e.g., U.S. Pat. No. 5,945,526 to Lee et al. Many of these dyes alsoare commercially available, for instance, from Molecular Probes Inc.(Eugene, Oreg.). Other dyes include Suitable donor fluorophores include6-carboxyfluorescein (FAM), tetrachloro-6-carboxyfluorescein (TET),2′-chloro-7′-phenyl-1,4-dichloro-6-carboxyfluorescein (VIC), and thelike.

In another embodiment, signal amplification may be achieved usinglabeled dendrimers as the detectable moiety (see, e.g., Physiol Genomics3:93-99, 2000). Fluorescently labeled dendrimers are available fromGenisphere (Montvale, N.J.). These may be chemically conjugated to theoligonucleotide primers by methods known in the art.

In another aspect the present invention provides kits for one of themethods described herein. The kit optionally contain buffers, enzymes,and reagents for amplifying the CFTR nucleic acid via primer-directedamplification. The kit also may include one or more devices fordetecting the presence or absence of particular mutant CF sequences inthe amplified nucleic acid. Such devices may include one or more probesthat hybridize to a mutant CF nucleic acid sequence, which may beattached to a bio-chip device, such as any of those described in U.S.Pat. No. 6,355,429. The bio-chip device optionally has at least onecapture probe attached to a surface on the bio-chip that hybridizes to amutant CF sequence. In preferred embodiments the bio-chip containsmultiple probes, and most preferably contains at least one probe for amutant CF sequence which, if present, would be amplified by a set offlanking primers. For example, if five pairs of flanking primers areused for amplification, the device would contain at least one CF mutantprobe for each amplified product, or at least five probes. The kit alsopreferably contains instructions for using the components of the kit.

The following examples serve to illustrate the present invention. Theseexamples are in no way intended to limit the scope of the invention

EXAMPLES Example 1: Sample Collection and Preparation

Whole Blood:

5 cc of whole blood is collected in a lavender-top (EDTA) tube oryellow-top (ACD) tube, Green-top (Na Heparin) tubes are acceptable butless desirable. DNA is extracted from blood. 100 ng or more DNA isprepared in TE or sterile water.

Amniotic Fluid:

10-15 cc of Amniotic Fluid is collected in a sterile plastic container.

Cultured Cells:

Two T-25 culture flasks with 80-100% confluent growth may be used.

Chorionic Villi:

10-20 mg of Chorionic Villi are collected in a sterile container. 2-3 mLof sterile saline or tissue culture medium is added.

Transport:

Whole Blood, Amniotic Fluid, Cultured Cells and Chorionic Villi can beshipped at room temperature (18°-26° C.). Amniotic Fluid, Cultured Cellsor Chorionic Villi preferably is used without refrigeration or freezing.Whole Blood and Extracted DNA can be shipped at 2°−10° C.

Storage:

Whole Blood, Amniotic Fluid and Extracted DNA are stored at 2°-10° C.,Cultured Cells and Chorionic Villi are stored at room temperature(18°-26° C.).

Stability:

Whole Blood is generally stable for 8 days at room temperature (18°-26°C.) or 8 days refrigerated at 2°−10° C. Amniotic Fluid, Cultured Cells,and Chorionic Villi are generally processed to obtain DNA within 24hours of receipt. Extracted DNA is stable for at least 1 year at 2°-10°C.

Example 2: Amplification from DNA

Polymerase chain reaction (PCR) primer pairs were designed using theCFTR gene sequences in EMBL/Genbank (Accession Nos. M55106-M55131). EachPCR primer for the 32 separate PCR reactions contains either an M13forward linker sequence or an M13 reverse linker sequence as appropriateto allow universal sequence reaction priming. Individual PCR reactionsare performed in 96-well microtiter plates under the same conditions foreach amplicon. Subsequently, the PCR products are purified with theMillipore Montage™ PCR₉₆ Cleanup kit (Millipore, Bedford, Mass.) on aBeckman BioMek 2,000 biorobot. Further details are provided in Strom etal., 2003 Genetics in Medicine 5(1):9-14.

In general, individual amplifications are prepared in a volume of 13.5μl, which is added to the 96 well microtiter plates. Each amplificationvolume contained 2 μl of the nucleic acid sample (generally 10-100 ng ofDNA), 11.5 μl of PCR-Enzyme Mix (PCR-Enzyme mix stock is prepared with11.3 μl master mix, 0.25 μl MgCl₂ (from 25 mM stock), and 0.2 μl ofFasStar Taq (source for last two reagents was Roche Applied science,Cat. No. 2 032 937). Master mix contained primers, Roche PCR buffer withMgCl₂, Roche GC rich solution (cat. No. 2 032 937), bovine serum albumin(BSA) (New England BioLabs, Cat no. B9001B), and NTPs (AmershamBiosciences, Cat no. 27-2032-01).

The final concentration in the PCR for MgCl₂ was 2.859 mM, for BSA is0.725 μg/μl, and for each dNTP is 0.362 mM. Primer final concentrationsvaried from about 0.29 μM to about 0.036 μM

PCR is conducted using the following temperature profile: step 1: 96° C.for 15 minutes; step 2: 94° C. for 15 seconds; step 3: decrease at 0.5°C./second to 56° C.; step 4: 56° C. for 20 seconds; step 5: increase at0.3° C./second to 72° C., step 6: 72° C. for 30 seconds; step 7:increase 0.5° C. up to 94° C.; step 8: repeat steps 2 to 7 thirty threetimes; step 9: 72° C. for 5 minutes; step 10: 4° C. hold (to stop thereaction).

Example 3: Detection of CF Mutations

The purified PCR products are diluted to approximately 10 ng/L and cyclesequencing reactions are performed with an ABI Prism Big Dye™ Terminatorv3.0 cycle sequencing reaction kit (Applied Biosystems, Foster City,Calif.) according to the manufacturer's protocol. The DNA primers usedfor the sequencing reaction are M13 forward and reverse primers asappropriate. Big Dye™ Terminator reaction products are purified by theMillipore Montage™ Seq₉₆ Sequencing Reaction Cleanup kit on a biorobotand analyzed on an ABI Prism 3100 Genetic Analyzer. Sequences obtainedare examined for the presence of mutations by using ABI SeqScape v1.1software. Both strands of DNA are sequenced.

All PCR reactions, purifications, and cycle sequencing reactions areperformed in 96-well microtiter plates using biorobots to avoid errorsintroduced by manual setups. Loading of samples onto the capillarysequencer is also automated. One plate is sufficient to perform theentire sequencing reaction for a single patient. Theoretically, if allreactions were successful, the entire sequences for a single patientcould be obtained in 24-48 hours after receipt of blood. In practice,however, one or more reactions must be repeated because of frequentpolymorphisms in intron 8 and 6a and failed reactions.

Example 4: Multiplex PCR Assay for CFTR Gene Segments

A. Extraction of DNA

Whole blood, amniotic fluid, cultured cells, and chorionic villi, aremaintained preferably under ambient temperature (18-26° C.). Whole bloodshould be stable for 8 days at ambient temperature (18-26° C.) or 8 daysrefrigerated (2-8° C.). Optimally, DNA should be extracted amnioticfluid, cultured cells, or chorionic villi within 24 hours of receipt.Samples are preferably analyzed without freezing. Once extracted, DNAshould be stable for 24-48 hours at 2-8° C. DNA should be frozen iflonger storage is anticipated.

The following example describes a suitable procedure to prepare nucleicacids from blood. 50 μL of whole blood is mixed with 0.5 ml of TE (10 mMTris HCl, 1 mM EDTA, pH 7.5) in a 1.5 mL microfuge tube. The sample isspun for 10 seconds at 13,000×g. The pellet is resuspended in 0.1 mL ofTE buffer with vortexing, and pelleted again. This procedure is repeatedtwice more, and then the final cell pellet is resuspended in 100 μl of Kbuffer 50 mM KCl, 10 mM Tris HCl, 2.5 mM MgCl₂, 0.5% Tween 20, 100 μg/mLproteinase K, pH 8.3) and incubated 45 minutes at 56° C., then 10minutes at 95° C. to inactivate the protease.

Alternative nucleic acid extraction methods can be used such as theQiagen extraction method (Qiagen BioRobot 9604).

B. Preparation of CFTR-Multiplex PCR Primer Mix

A multiplex PCR that can verify a suspected CFTR promoter deletion orduplication and assess the extent of such deletion or duplication may beperformed using the mixture of primers shown in Table 5. The amount ofeach primer in the amplification is listed in Table 5 along with theexpected size of the fragment. The promoter deletion/duplicationverification PCR primer mix (1,025 μL) was made by mixing stocksolutions (100 μM) of each of the primers shown in Table 5. Thesequences of these primers can be found in Tables 1 and 2. In additionto the three promoter primers upstream of the first promoter primer set,the master mix includes primers for the three internal controls andprimer pairs for CFTR exons 1-4.

TABLE 5 CFTR promoter deletion/duplication verification primer mastermix. x 1 rxn Final Conc in PCR Size Primer Name (ul) 200 Reaction uMExpected TSF 0.05 10 0.2 140 TSR 0.05 10 0.2 F2F 0.05 10 0.2 332 F2R0.05 10 0.2 F5F 0.05 10 0.2 212 F5R 0.05 10 0.2 UpPr1F 0.05 10 0.2 230UpPr1R 0.05 10 0.2 CFDEL3F2 0.025 5 0.1 132 CFDEL3R 0.025 5 0.1 UpPr2F10.025 5 0.1 202 UpPr2R 0.025 5 0.1 CFDEL2F 0.025 5 0.1 154 CFDEL2R 0.0255 0.1 UpPr3F 0.025 5 0.1 188 UpPr3R 0.025 5 0.1 CFDEL4F 0.0375 7.5 0.15237 CFDEL4R 0.0375 7.5 0.15 CFDEL1F 0.075 15 0.3 272 CFDEL1R 0.075 150.3 CFDELPF 0.075 15 0.3 287 CFDELPR 0.075 15 0.3 Total 1.025 205

C. Amplification from DNA

Individual amplifications were prepared in a volume of 25 μl. Eachamplification volume contained 4 μl of the DNA sample (generally 10-100ng of DNA), 20.6 μl of CFTR Master Mix, and 0.4 μl of FasStar Taq (RocheApplied science, Cat. No. 2 032 937). In another approach, individualamplifications were prepared in a volume of 12.5 μl. Each amplificationvolume contained 2 μl of the DNA sample (generally 10-100 ng/μl of DNA),10.3 μl of CFTR master mix and 0.2 μl of FasStar Taq (Roche AppliedScience, Cat no. 2032937).

Master mix contained the CFTR-multiplex PCR primer mix, Roche PCR bufferwith MgCl₂, Roche GC rich solution (cat. No. 2 032 937), bovine serumalbumin (BSA) (New England BioLabs, Cat no. B9001B), and NTPs (AmershamBiosciences, Cat no. 27-2032-01). The final concentration in the PCR forMgCl₂ was 2.859 mM, for BSA was 0.725 μg/μl, and for each dNTP was 0.362mM. The PCR master mix for the full multiplex of primers in Table 1 isshown in Table 6. The PCR master mix for the full multiplex of promoterregion primers and controls in Tables 2 is shown in Table 7. Theconcentration of individual primers fell in the range 0.1 to 0.4 μM.

TABLE 6 CFTR PCR master mix X 1 rxn Final Conc in PCR Reagent (ul) 1000Reaction mM FS 10X w/o MgCl₂ 5 5000 2X MgCl₂ 4 4000 4   25 mM dNTP 0.4400 0.4 Primer MIX 4.55 4550 GC rich 2.5 2500 1X BSA (10 mg/ml) 1 10000.4 ug/ul Water 3.15 3150 Total 20.6 20600

TABLE 7 CFTR Promoter region Master mix x 1 rxn Final Conc in PCRReagent (ul) 200 Reaction mM FS 10X w/o MgCl2 2.5 500 2X MgCl2 2 400 2  25 mM dNTP 0.2 40 0.2 Primer MIX 1.025 205 GC rich 1.25 250 1X BSA (10mg/ml) 0.5 100 0.4 ug/ul Water 2.825 565 Total 10.3 2060

PCR was conducted using the following temperature profile: step 1: 95°C. for 5 minutes; step 2: 94° C. for 15 seconds; step 3: decrease at0.5° C./second to 56° C.; step 4: 56° C. for 1 minute and 10 seconds;step 5: increase at 0.5° C./second to 72° C., step 6: 72° C. for 45seconds+5 seconds additional per additional cycle; step 7: increase 0.5°C. up to 94° C.; step 8: repeat steps 2 to 7 twenty one times; step 9:72° C. for 5 minutes; step 10: 60° C. for 75 min, step 11: 4° C. hold(to stop the reaction).

D. Detection and Analysis of Amplified Product

2 μL of each PCR product was added to 10.5 μL Hi-Di-Rox 350 mix andloaded onto a ABI 3100 Genetic Analyzer for separation. Alternatively,electrophoresis can be performed by subjecting the amplified product togel electrophoresis such as an agarose gel electrophoresis. The primersmay need to be labeled with a detectable label to enhance thesensitivity of detection in some gel systems.

The data corresponding to the amplified nucleotide segments from theABI3100 were analyzed using GeneMapper software. The observed size andcolor of each target segment amplified from normal DNA using the primerset shown in Table 1 is shown in Table 8. FAM is blue and HEX is green.

TABLE 8 Analysis of amplified CFTR exons and internal controls CFTRexon/intron or internal control Size Observed size DYE UpEx 9 118 113.6Green Ex 3 128 124.2 Blue Ex 11 132 127.2 Blue Ex 21 136 132.7 BlueTay-Sachs 140 137.6 Green Ex 14a 144 142.1 Blue Ex 2 154 153 Blue Ex 5159 157.4 Blue Ex 20 162 161.8 Blue Ex 6a 170 170.4 Blue Ex 22 176 176.6Blue Ex 24 187 183.6 Blue Ex 17a 190 188.4 Blue Ex 23 193 191.6 Blue Ex14b 201 200.3 Blue Ex 12 208 205.9 Blue Factor 5 212 210.4 Green Ex 8216 215 Blue Ex 6b 228 226.8 Blue Ex 4 237 236.9 Blue Ex 10 245 245.5Blue Ex 19 250 248.7 Blue Ex 13 253 253.3 Blue Ex 15 262 261.6 Blue Ex 7267 267.1 Blue Ex 1 272 272 Blue Ex 16 281 280.9 Blue Promoter 287 288.2Blue Ex 18 297 296.1 Blue Ex 17b 306 303.9 Blue Ex 9 318 317.4 BlueFactor 2 332 331.9 Blue

The signal for each of the above amplicons observed for DNA from asample with an unknown CFTR genotype is compared with the amount of thecorresponding amplified segment observed for DNA from an individual witha wildtype CFTR gene. The GeneMapper software is used to analyze datagenerated from the ABI 3100. An Excel report is uploaded into a databasethat will score the results and generate automated allele calls.

A deletion of one or more exons will be shown by a drop in the intensityof the fragment(s) by at least 30-50%, of the normal (wildtype CFTRexon) signal while a duplication will show an increase to at least130-150% of the normal (wildtype CFTR exon) signal.

For best results, sample DNA for unknown CFTR genotype should beamplified in parallel with positive control sample containing wt/wt CFTRgenotype and/or wt/mut genotype for CF carriers.

Negative controls included;

a) NS Control: a reagent blank (NS control) comprises all reagents andprocessing used to prepare sample DNA but without any starting DNA; and

b) ND Control: A minus DNA control (ND control) is used which consistsof a PCR kit and polymerase mix used for the assay run.

Positional Control: a QC blank is placed randomly within each plate toensure results reflect the correct positioning of the Extraction/PCRplate for detection.

Negative controls should display no significant amplification and/orfluorescent signal. If the reagent blank (NS control) shows evidence ofsignificant amplification, all the patient samples associated with thatNS control are potentially contaminated. If the minus DNA control (NDcontrol) yields significant amplification, the PCR amplificationreagents are potentially contaminated. Note that the existing PCR masterreaction mix may be the source of the contamination. Specimens my needto be re-extracted and re-assayed (NS) and the entire assay repeated(ND).

Negative control DNAs should display no significant fluorescent signalupon electrophoresis on an ABI3100 genetic analyzer. If the NS controlshows evidence of significant fluorescence, all the patient samplesassociated with that NS control are potentially contaminated.

The QC Blank control should display no significant signal.

Example 5: Evaluating Samples from Individuals to Determine a GeneticBasis for CF

Samples from patients with a mutant CF gene were evaluated for CFdeletion or duplication analysis in accordance with the methods herein.Several samples with rearrangements were identified. A deletionencompassing the CFTR promoter, and exons 1 and 2 was detected in onesample, with the same mutation detected in the maternal DNA. In anotherfamily, a deletion of the promoter and exon 1 was detected in threesiblings. In both of these cases, the families were African-American,and a 3120+1G>A splice site mutation was identified. These deletionshave not been previously described. In a third case involving aCaucasian patient, a deletion of exons 17a, 17b and 18 was identifiedand the same mutation was detected in the paternal DNA. In four othercases, deletions in exons 2 and 3; exons 4, 5 and 6a; exons 17a and 17b;and a deletion of exons 22, 23 and 24 were identified. These mutationswould remove parts of transmembrane domain 1, transmembrane domain 2, orthe second Nucleotide Binding Domain. In patients diagnosed with“classic CF” submitted for sequencing analysis, 20% harboredrearrangements, accounting for 10% of CF chromosomes. Classic CF ischaracterized by elevated sweat chloride, lung and pancreaticinsufficiency, failure to thrive, and in most male cases, and congenitalbilateral absence of the vas deferens (CBAVD). The frequency ofoccurrence of rearrangements in CF patients when only one mutation isidentified by DNA sequencing is 50%. It is possible that complexabnormalities may account for a significant proportion of CF chromosomesin the general population.

Example 6: Clinical Presentation of Dup Ex 6b-10 (IVS6a+415IVS10+2987Dup26817 bp)

Phenotype details: The patient is a 19 year old, Caucasian female with adiagnosis of cystic fibrosis. She was born with meconium ileus and hasan elevated sweat chloride test of 110, pulmonary disease and livercirrhosis. She had a similarly affected sister who is deceased. Previousmutation testing had revealed the heterozygous presence of deltaF508that was inherited from her mother. DNA Sequencing did not identifysecond mutation, Analysis by SQF PCR of fragments representing thepromoter and all CFTR exons identified a tandem duplication of exons6b-10. DNA Sequencing verified the presence of the duplication bydetecting a fusion of IVS10 to IVS6a.

Nucleotide change: A duplication of exons 6b-10. The duplication is26,817 bp long.

Exon: Duplication of Exons 6b-10.

Consequence: Out-of-frame fusion of exon 10 to exon 6b. The duplicationwould cause an out-of-frame addition if 8 amino acids after codon E528of Exon 10, followed by a TGA Stop codon. The result is a truncatedprotein lacking terminal NBD1 and beyond.

Example 7: Detecting Dup Ex 6b-10 with Primers Flanking the JunctionSite

This example demonstrates identification of the exon 6b-10 mutation innucleic acid from the patient discussed in Example 6. FIG. 2 shows aschematic of the CFTR gene with arrows depicting the general location offorward and reverse PCR primers flanking the unique junctionIVS10+2,987/IVS6a+415. PCR across the junction was achieved using aforward primer from exon 10 located in intron 9(5′-TGTAAAACGACGGCCAGTagcagagtacctgaaacagga-3′; SEQ ID NO: 89) and areverse primer for exon 6b located in intron 6b(5′-CAGGAAACAGCTATGACCGTGGAAGTCTACCATGATAAACATA-3′; SEQ ID NO: 90).Following PCR a single product was observed on an agarose gel, runningjust below a 4.6 kb standard.

The contents of the articles, patents, and patent applications, and allother documents and electronically available information mentioned orcited herein, are hereby incorporated by reference in their entirety tothe same extent as if each individual publication was specifically andindividually indicated to be incorporated by reference.

Applicants reserve the right to physically incorporate into thisapplication any and all materials and information from any sucharticles, patents, patent applications, or other physical and electronicdocuments.

The inventions illustratively described herein may suitably be practicedin the absence of any element or elements, limitation or limitations,not specifically disclosed herein. Thus, for example, the terms“comprising”, “including,” containing”, etc. shall be read expansivelyand without limitation. Additionally, the terms and expressions employedherein have been used as terms of description and not of limitation, andthere is no intention in the use of such terms and expressions ofexcluding any equivalents of the features shown and described orportions thereof, but it is recognized that various modifications arepossible within the scope of the invention claimed. Thus, it should beunderstood that although the present invention has been specificallydisclosed by preferred embodiments and optional features, modificationand variation of the inventions embodied therein herein disclosed may beresorted to by those skilled in the art, and that such modifications andvariations are considered to be within the scope of this invention.

The invention has been described broadly and generically herein. Each ofthe narrower species and subgeneric groupings falling within the genericdisclosure also form part of the invention. This includes the genericdescription of the invention with a proviso or negative limitationremoving any subject matter from the genus, regardless of whether or notthe excised material is specifically recited herein. Other embodimentsare within the following claims. In addition, where features or aspectsof the invention are described in terms of Markush groups, those skilledin the art will recognize that the invention is also thereby describedin terms of any individual member or subgroup of members of the Markushgroup.

1.-21. (canceled)
 22. A kit comprising: (i) a forward primer thatcomprises the sequence of SEQ ID NO: 89 and a reverse primer thathybridizes to intron 6b or exon 6b of the CFTR gene; or (ii) a forwardprimer that hybridizes to intron 9 or exon 10 of the CFTR gene and areverse primer that comprises the sequence of SEQ ID NO: 90, wherein theforward primer or reverse primer is detectably labeled.
 23. The kit ofclaim 22, further comprising a nucleic acid probe that binds to anamplification product produced by the forward primer and the reverseprimer.
 24. The kit of claim 23, wherein the nucleic acid probe isdetectably labeled.
 25. The kit of claim 23, wherein the nucleic acidprobe spans a junction site between exons 10 and 6b resulting from aduplication of exon 6b through exon 10 of the CFTR gene.
 26. The kit ofclaim 23, wherein the nucleic acid probe spans a IVS10+2,987/IVS6a+415junction site.
 27. The kit of claim 23, wherein the nucleic acid probecomprises the sequence of SEQ ID NO:2.
 28. The kit of claim 23, whereinthe nucleic acid probe comprises the sequence of SEQ ID NO:3.
 29. Thekit of claim 23, wherein the nucleic acid probe comprises the sequenceof SEQ ID NO:4.
 30. The kit of claim 22, wherein the forward primercomprises the sequence of SEQ ID NO: 89 and the reverse primer comprisesthe sequence of SEQ ID NO:
 90. 31. The kit of claim 22, wherein theforward primer and/or reverse primer are detectably labeled with afluorescent dye.
 32. The kit of claim 23, wherein the nucleic acid probeis detectably labeled with a fluorescent dye.
 33. The kit of claim 22,wherein the forward primer and reverse primer are present together in anamplification master mix that further comprises DNA polymerase, dNTPsand PCR buffer.
 34. A kit comprising: (a) a primer pair comprising: (i)a forward primer that comprises the sequence of SEQ ID NO: 89 and areverse primer that hybridizes to intron 6b or exon 6b of the CFTR gene;or (ii) a forward primer that hybridizes to intron 9 or exon 10 of theCFTR gene and a reverse primer that comprises the sequence of SEQ ID NO:90; and (b) a detectably labeled nucleic acid probe that that binds toan amplification product produced by the forward primer and the reverseprimer.
 35. The kit of claim 34, wherein the detectably labeled nucleicacid probe spans a junction site between exons 10 and 6b resulting froma duplication of exon 6b through exon 10 of the CFTR gene.
 36. The kitof claim 34, wherein the detectably labeled nucleic acid probe spans aIVS10+2,987/IVS6a+415 junction site.
 37. The kit of claim 34, whereinthe detectably labeled nucleic acid probe comprises the sequence of SEQID NO:2, 3, or
 4. 38. The kit of claim 34, wherein the forward primercomprises the sequence of SEQ ID NO: 89 and the reverse primer comprisesthe sequence of SEQ ID NO:
 90. 39. The kit of claim 34, wherein theforward primer, reverse primer, and/or probe are present together in anamplification master mix that further comprises DNA polymerase, dNTPsand PCR buffer.
 40. The kit of claim 34, wherein the nucleic acid probeis detectably labeled with a fluorescent dye.
 41. The kit of claim 34,wherein the forward primer and/or reverse primer are detectably labeledwith a fluorescent dye.